dbSNP rs2076605: ATP13A2:c.3236-30C>T (chr1-16986662-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022089.4(ATP13A2):c.3236-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,587,734 control chromosomes in the GnomAD database, including 200,655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 14622 hom., cov: 30)

Exomes 𝑓: 0.50 ( 186033 hom. )

Consequence

ATP13A2
NM_022089.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.13

Variant links:

Genes affected

ATP13A2 (HGNC:30213): (ATPase cation transporting 13A2) This gene encodes a member of the P5 subfamily of ATPases which transports inorganic cations as well as other substrates. Mutations in this gene are associated with Kufor-Rakeb syndrome (KRS), also referred to as Parkinson disease 9. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2008]

ATP13A2 links:

ENSG00000226526 (HGNC:):

ENSG00000226526 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 1-16986662-G-A is Benign according to our data. Variant chr1-16986662-G-A is described in ClinVar as [Benign]. Clinvar id is 559000.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-16986662-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP13A2	NM_022089.4 link	c.3236-30C>T		intron_variant	Intron 27 of 28	ENST00000326735.13	NP_071372.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP13A2	ENST00000326735.13 link	c.3236-30C>T		intron_variant	Intron 27 of 28	1	NM_022089.4	ENSP00000327214.8		Q9NQ11-1

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63323

AN:

151670

Hom.:

14617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.447

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.281

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.527

Gnomad OTH

AF:

0.431

GnomAD3 exomes

AF:

0.471

AC:

98011

AN:

208288

Hom.:

23501

AF XY:

0.476

AC XY:

54220

AN XY:

113908

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.484

Gnomad ASJ exome

AF:

0.482

Gnomad EAS exome

AF:

0.296

Gnomad SAS exome

AF:

0.477

Gnomad FIN exome

AF:

0.487

Gnomad NFE exome

AF:

0.524

Gnomad OTH exome

AF:

0.476

GnomAD4 exome

AF:

0.504

AC:

724300

AN:

1435946

Hom.:

186033

Cov.:

AF XY:

0.504

AC XY:

359756

AN XY:

713304

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.477

Gnomad4 ASJ exome

AF:

0.484

Gnomad4 EAS exome

AF:

0.308

Gnomad4 SAS exome

AF:

0.473

Gnomad4 FIN exome

AF:

0.486

Gnomad4 NFE exome

AF:

0.527

Gnomad4 OTH exome

AF:

0.474

GnomAD4 genome

AF:

0.417

AC:

63340

AN:

151788

Hom.:

14622

Cov.:

AF XY:

0.413

AC XY:

30628

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.447

Gnomad4 ASJ

AF:

0.473

Gnomad4 EAS

AF:

0.281

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.473

Gnomad4 NFE

AF:

0.527

Gnomad4 OTH

AF:

0.426

Alfa

AF:

0.451

Hom.:

3376

Bravo

AF:

0.407

Asia WGS

AF:

0.342

AC:

1190

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 19, 2015

Mayo Clinic Laboratories, Mayo Clinic

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 06, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 69% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 64. Only high quality variants are reported. -

Autosomal recessive spastic paraplegia type 78

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Kufor-Rakeb syndrome

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over